BN0655 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 8.3027e-07 3.7272e-03
Layer 4 9.3194e-07 6.2017e-05
Layer 5 3.3455e-06 1.6935e-04
Layer 6 7.8954e-05 2.7988e-04
Layer 2 1.1610e-03 1.9149e-01
Layer 1 8.8827e-01 6.0721e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.2578 0.7887
NCOA7 Layer 5 2.4541 0.7457
ELAVL2 Layer 4 2.7070 0.7319
SATB1 Layer 4 2.8027 0.7312
PCLO Layer 6 2.5059 0.7271
SSBP3 Layer 5 2.6953 0.7251
SH3GL2 Layer 4 2.3340 0.7246
CPLX1 Layer 4 2.4121 0.7217
ELAVL4 Layer 4 2.6484 0.7149
SV2B Layer 5 2.1914 0.7143
PTPA Layer 5 2.3281 0.7125
GNAO1 Layer 5 2.1797 0.7124
TRIM37 Layer 4 2.4180 0.7102
TBR1 Layer 6 2.8828 0.7094
STX1A Layer 5 2.6133 0.7092
FLOT1 Layer 5 2.2803 0.7079
NUAK1 Layer 4 2.4941 0.7065
SLIT1 Layer 6 2.9609 0.7058
SLC24A2 Layer 4 2.6777 0.7056
ATXN7L3 Layer 5 2.3555 0.7052
FLOT2 Layer 5 2.1816 0.7045
SPOCK1 Layer 6 2.5957 0.7042
SYT4 Layer 6 2.5117 0.7042
CNTNAP1 Layer 4 2.3398 0.7039
UBE2V2 Layer 5 2.2773 0.7038
CEND1 Layer 6 2.2930 0.7029
KCNA2 Layer 4 2.3594 0.7005
IQSEC1 Layer 5 2.3623 0.6982
MEF2C Layer 4 2.1289 0.6974
CTSD Layer 5 2.2363 0.6966
HK1 Layer 5 2.3184 0.6962
EPS15 Layer 5 2.4102 0.6956
MCRIP1 Layer 5 2.4570 0.6956
RORB Layer 4 3.3438 0.6953
SNAP91 Layer 4 2.4238 0.6951
SYNGR1 Layer 5 2.3555 0.6946
ADD1 Layer 5 2.1445 0.6935
QDPR Layer 5 2.3711 0.6930
CLDND1 Layer 6 2.5059 0.6930
NCALD Layer 6 2.7793 0.6928
STX1B Layer 5 2.3184 0.6928
PFKP Layer 5 2.5000 0.6928
IPCEF1 Layer 4 2.9863 0.6917
LSAMP Layer 4 2.2715 0.6914
TUBA4A Layer 5 2.2715 0.6905
PRUNE2 Layer 5 2.4727 0.6904
SULT4A1 Layer 4 2.3281 0.6904
TUBB4A Layer 6 2.0957 0.6899
PRKCZ Layer 6 2.4238 0.6890
DCTN1 Layer 5 2.1680 0.6883

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0655
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0655_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0655/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0655/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0655/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0655/report/PD/BN0655_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0655/report/PD/BN0655_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:06:28
  • Number of Processes: 10
  • Spending Time: 0h 2m